12th-15th June 2023
To foster international participation, this course will be held online
General Topic: Evolution of transposable elements and their bioinformatic analysis
Transposable elements (TEs) are selfish genetic elements which exist in virtually all eukaryotic genomes. Because TEs contain regulatory or coding sequences for their own ‘survival’ and often
occur in large numbers within a genome, they can have strong effects on the transcription or the epigenetic regulation of nearby genes and significantly promote structural variation or genome
size expansion. The analysis of TEs is thus important for many studies in genomics and evolutionary biology. However, TEs are rapidly evolving due to arms races with their host genomes and thus
often remain undetected in newly sequenced genomes. One may argue that in-depth annotation of TEs is currently one of the biggest bottlenecks in genomics research of non-model organisms.
Furthermore, their repeatedness makes them challenging to study using conventional bioinformatic tools. Indeed, computational TE analyses require knowledge of TE biology as well as
awareness of the pitfalls to overcome in diverse applications (genome annotation, TE classification, insertions polymorphism, transcriptomics) . The present course aims to address these
challenges by teaching TE biology, computational analyses of TEs in genome assemblies and raw read data (building de-novo TE library, TE quantification, Insertion polymorphism) as well as
transcriptomics (differential expression of TE families), and the manual analyses of TEs (consensus curation, classification).
At the end of this course, attendants should be able to conduct computational analyses of TEs, interpret the results in the light of TE biology, and improve TE annotations through manual
curation. The participants will also have the opportunity to discuss their own projects and receive guidance regarding TE analysis. To achieve this, each day will be composed of lectures on TE
biology and practical sessions covering diverse bioinformatic analyses. Each day will be concluded with an informal and facultative open discussion regarding the themes covered in the class. The
last day will include a dedicated session where attendees will be able to explore strategies related to their own project and further refine their skills in computational and manual
analyses of TEs.
The course is aimed at biologists at any career stage who are new to TE analyses and/or de-novo annotation of the repetitive fraction of non-model genomes.
Attendants will need to use the command line (UNIX/Shell on Linux and MacOS, Cygwin on Windows) and a sequence alignment program (e.g., BioEdit, AliView) on their computer. Basic knowledge of
these will be helpful but is not required. Attendants are encouraged to bring their own genome assembly raw read and/or transcriptomic data, though this will not be required to take advantage of
the training.
Monday - 2-7 pm Berlin time
Course Introduction
Lecture 1: “TE diversity and mechanisms”
Lecture 2: “TE discovery and annotation”
“TE social club”: open discussion, personal project presentation.
Tuesday- 2-7 pm Berlin time
Lecture 3: “TE classification and manual curation”
Practical 1: Automatic discovery and annotation of TEs
Practical 2: Manual curation of TE libraries
“TE social club”: open discussion
Wednesday- 2-7 pm Berlin time
Lecture 4: “TEs and genome evolution”
Practical 3: Insertion polymorphism
“TE social club”: open discussion
Thursday- 2-7 pm Berlin time
Lecture 4: “TEs functional genomics”
Practical 4: TE expression analysis
Personal Projects Q&A
“TE social club”: open discussion
480 €
Cancellation Policy:
> 30 days before the start date = 30% cancellation fee
< 30 days before the start date= No Refund.
Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.